Elbow Plot for Clustering

Heatmap

Number of Genes

Cluster Enrichments

Ectoderm Cluster

## Uploading data to Enrichr... Done.
##   Querying KEGG_2019... Done.
##   Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.

GO_Biological_Process_2018

KEGG_2019

Neuroectoderm Cluster

## Uploading data to Enrichr... Done.
##   Querying KEGG_2019... Done.
##   Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.

GO_Biological_Process_2018

KEGG_2019

Mesoderm Cluster

## Uploading data to Enrichr... Done.
##   Querying KEGG_2019... Done.
##   Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.

GO_Biological_Process_2018

KEGG_2019

Overlap between targets downregulated in WT vs. LOF and all clusters

Venn Diagram

Upset Plot

Resampling

Mesoderm

n
## [1] 50000
sum(res > 739)/n
## [1] 0

Neuroectoderm

n
## [1] 50000
sum(res > 292)/n
## [1] 0

Ectoderm

n
## [1] 50000
sum(res > 161)/n
## [1] 1

Overlap Enrichments

Downregulated & Neuroectoderm Overlap

## Uploading data to Enrichr... Done.
##   Querying KEGG_2019... Done.
##   Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.

Downregulated & Mesoderm Overlap

## Uploading data to Enrichr... Done.
##   Querying KEGG_2019... Done.
##   Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.

Mesoderm only

## Uploading data to Enrichr... Done.
##   Querying KEGG_2019... Done.
##   Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.

Neuroectoderm only

## Uploading data to Enrichr... Done.
##   Querying KEGG_2019... Done.
##   Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.

Downregulated only

## Uploading data to Enrichr... Done.
##   Querying KEGG_2019... Done.
##   Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.

Overlap between targets UPREGULATED in WT vs. LOF and all clusters

Venn Diagram

Upset Plot

Resampling

Mesoderm

n
## [1] 50000
sum(res > 223)/n
## [1] 1

Neuroectoderm

n
## [1] 50000
sum(res > 109)/n
## [1] 0.99942

Ectoderm

n
## [1] 50000
sum(res > 629)/n
## [1] 0

Overlap Enrichments

Upregulated & Ectoderm Overlap

## Uploading data to Enrichr... Done.
##   Querying KEGG_2019... Done.
##   Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.

Ectoderm only

## Uploading data to Enrichr... Done.
##   Querying KEGG_2019... Done.
##   Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.

Upregulated only

## Uploading data to Enrichr... Done.
##   Querying KEGG_2019... Done.
##   Querying GO_Biological_Process_2018... Done.
## Parsing results... Done.

Combined Upset Plot

Other Venn Diagrams

Session Info

## R version 4.1.1 (2021-08-10)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur 10.16
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
##  [1] grid      parallel  stats4    stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] png_0.1-7                             UpSetR_1.4.0                         
##  [3] enrichR_3.0                           VennDiagram_1.6.20                   
##  [5] futile.logger_1.4.3                   org.Dm.eg.db_3.13.0                  
##  [7] msigdbr_7.4.1                         cowplot_1.1.1                        
##  [9] ggpubr_0.4.0                          data.table_1.14.0                    
## [11] DT_0.19                               forcats_0.5.1                        
## [13] dplyr_1.0.7                           purrr_0.3.4                          
## [15] readr_2.0.1                           tidyr_1.1.3                          
## [17] tibble_3.1.4                          tidyverse_1.3.1                      
## [19] factoextra_1.0.7                      ggplot2_3.3.5                        
## [21] cluster_2.1.2                         stringr_1.4.0                        
## [23] BSgenome.Dmelanogaster.UCSC.dm6_1.4.1 BSgenome_1.60.0                      
## [25] rtracklayer_1.52.1                    Biostrings_2.60.2                    
## [27] XVector_0.32.0                        pheatmap_1.0.12                      
## [29] geneplotter_1.70.0                    annotate_1.70.0                      
## [31] XML_3.99-0.7                          reshape_0.8.8                        
## [33] lattice_0.20-44                       gridExtra_2.3                        
## [35] RColorBrewer_1.1-2                    GenomicFeatures_1.44.2               
## [37] AnnotationDbi_1.54.1                  knitr_1.33                           
## [39] DESeq2_1.32.0                         SummarizedExperiment_1.22.0          
## [41] Biobase_2.52.0                        MatrixGenerics_1.4.3                 
## [43] matrixStats_0.60.1                    GenomicRanges_1.44.0                 
## [45] GenomeInfoDb_1.28.4                   IRanges_2.26.0                       
## [47] S4Vectors_0.30.0                      BiocGenerics_0.38.0                  
## 
## loaded via a namespace (and not attached):
##   [1] readxl_1.3.1             backports_1.2.1          BiocFileCache_2.0.0     
##   [4] plyr_1.8.6               splines_4.1.1            crosstalk_1.1.1         
##   [7] BiocParallel_1.26.2      digest_0.6.27            htmltools_0.5.2         
##  [10] fansi_0.5.0              magrittr_2.0.1           memoise_2.0.0           
##  [13] tzdb_0.1.2               openxlsx_4.2.4           modelr_0.1.8            
##  [16] prettyunits_1.1.1        colorspace_2.0-2         blob_1.2.2              
##  [19] rvest_1.0.1              rappdirs_0.3.3           ggrepel_0.9.1           
##  [22] haven_2.4.3              xfun_0.25                crayon_1.4.1            
##  [25] RCurl_1.98-1.4           jsonlite_1.7.2           genefilter_1.74.0       
##  [28] survival_3.2-11          glue_1.4.2               gtable_0.3.0            
##  [31] zlibbioc_1.38.0          DelayedArray_0.18.0      car_3.0-11              
##  [34] abind_1.4-5              scales_1.1.1             futile.options_1.0.1    
##  [37] DBI_1.1.1                rstatix_0.7.0            Rcpp_1.0.7              
##  [40] xtable_1.8-4             progress_1.2.2           foreign_0.8-81          
##  [43] bit_4.0.4                htmlwidgets_1.5.4        httr_1.4.2              
##  [46] ellipsis_0.3.2           farver_2.1.0             pkgconfig_2.0.3         
##  [49] dbplyr_2.1.1             locfit_1.5-9.4           utf8_1.2.2              
##  [52] labeling_0.4.2           tidyselect_1.1.1         rlang_0.4.11            
##  [55] munsell_0.5.0            cellranger_1.1.0         tools_4.1.1             
##  [58] cachem_1.0.6             cli_3.0.1                generics_0.1.0          
##  [61] RSQLite_2.2.8            broom_0.7.9              evaluate_0.14           
##  [64] fastmap_1.1.0            yaml_2.2.1               babelgene_21.4          
##  [67] bit64_4.0.5              fs_1.5.0                 zip_2.2.0               
##  [70] KEGGREST_1.32.0          formatR_1.11             xml2_1.3.2              
##  [73] biomaRt_2.48.3           compiler_4.1.1           rstudioapi_0.13         
##  [76] filelock_1.0.2           curl_4.3.2               ggsignif_0.6.2          
##  [79] reprex_2.0.1             stringi_1.7.4            highr_0.9               
##  [82] Matrix_1.3-4             vctrs_0.3.8              pillar_1.6.2            
##  [85] lifecycle_1.0.0          jquerylib_0.1.4          bitops_1.0-7            
##  [88] R6_2.5.1                 BiocIO_1.2.0             rio_0.5.27              
##  [91] lambda.r_1.2.4           assertthat_0.2.1         rprojroot_2.0.2         
##  [94] rjson_0.2.20             withr_2.4.2              GenomicAlignments_1.28.0
##  [97] Rsamtools_2.8.0          GenomeInfoDbData_1.2.6   hms_1.1.0               
## [100] rmarkdown_2.10           carData_3.0-4            lubridate_1.7.10        
## [103] restfulr_0.0.13